-N 100 hinder NanoCount accuracy?

[callumparr]

I used the following command from minimap2

minimap2 -t 4 -ax map-ont -p 1.0 -N 100 -k14 -uf index/transcriptome_index.mmi

In the readme, it is recommended to use -N 10. Would having potentially more secondary alignments hinder the NanoCount accuracy?

Ideally, I would not like to remap all my samples again as just want to see a comparison of salmon vs NanoCount for each sample.

[Josie Gleeson]

Hi,

I wouldn't worry. NanoCount will filter out any secondary alignments that aren't very good/nearly as good as the primary alignment. So it shouldn't affect your results.

[callumparr]

Thank you 🙏